Variant report

Variant	rs478061
Chromosome Location	chr9:101930993-101930994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101918300..101922228-chr9:101930528..101933247,3	K562	blood:
2	chr9:101921262..101923800-chr9:101929228..101931291,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1013186	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10283455	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10448292	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733709	0.94[CEU][hapmap]
rs10739779	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10760670	0.89[CEU][hapmap]
rs10760671	0.94[CEU][hapmap]
rs10760672	0.94[CEU][hapmap]
rs10760673	0.94[CEU][hapmap]
rs10760674	0.89[EUR][1000 genomes]
rs10819637	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10819638	0.94[CEU][hapmap]
rs10819639	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988703	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10988706	0.94[CEU][hapmap]
rs10988714	1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10988716	0.94[CEU][hapmap]
rs10988723	0.87[EUR][1000 genomes]
rs10988748	1.00[CHD][hapmap]
rs12345675	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13286149	1.00[ASN][1000 genomes]
rs1571589	0.89[CEU][hapmap]
rs1571590	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1590	0.95[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs1973518	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2026811	0.89[CEU][hapmap]
rs334348	0.95[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs334349	0.95[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs334350	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs334351	0.91[EUR][1000 genomes]
rs334353	0.80[ASW][hapmap];1.00[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs334354	0.94[CEU][hapmap]
rs334355	0.89[CEU][hapmap]
rs334356	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs334357	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs334358	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs334366	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs334368	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334369	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383496	0.88[EUR][1000 genomes]
rs385057	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs420549	0.94[CEU][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs44466	0.96[AFR][1000 genomes]
rs597457	0.94[CEU][hapmap]
rs6478972	0.89[CEU][hapmap]
rs7031302	0.82[CEU][hapmap]
rs7042852	1.00[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs7874221	0.94[CEU][hapmap]
rs789675	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs868	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893619	chr9:101835165-101936231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs478061	TGFBR1	cis	cerebellum	SCAN
rs478061	LOC286359	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101912600-101932200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:101922800-101932200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:101929400-101931000	Enhancers	Primary B cells from peripheral blood	blood
4	chr9:101929600-101931000	Enhancers	Fetal Thymus	thymus
5	chr9:101929600-101932200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:101929800-101933600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:101930000-101931800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:101930000-101932400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr9:101930000-101932400	Weak transcription	K562	blood
10	chr9:101930000-101933000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr9:101930200-101931600	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr9:101930200-101931600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr9:101930400-101931400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:101930400-101932400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr9:101930400-101933200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr9:101930400-101936600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:101930600-101931000	Enhancers	H9 Cell Line	embryonic stem cell
18	chr9:101930600-101931800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr9:101930600-101932400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr9:101930800-101931000	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr9:101930800-101931600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:101930800-101936000	Weak transcription	GM12878-XiMat	blood

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